The state’s highest court appeared to struggle Wednesday with how to resolve the more than 24,000 criminal convictions tied to disgraced drug chemist Annie Dookhan during arguments in the final legal battle of the case.

Several Supreme Judicial Court justices appeared hesitant to embrace a proposal to dismiss all the cases tied to Dookhan, but the justices also acknowledged the state’s failure to address the possibility that people have been convicted on tainted evidence in more than four years of litigation.

Lawyers for the criminal defendants argued that the full dismissal of the cases is the only way to ensure justice for each defendant and restore confidence in the integrity of the criminal justice system.

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Chief Justice Ralph D. Gants asked lawyers representing the defendants to define the principle the court should identify in the case: Should the court dismiss a criminal case any time there is evidence of wrongdoing by a drug lab chemist? If not, why should they do so now?

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“Would the principle be different if there were only 40 cases?” Gants asked.

“Yes,” Segal responded, in one of the several exchanges during the hearing. “One case can be handled, 40 cases can be handled, 24,000 cases cannot.”

Later, Susanne M. O’Neil, an assistant district attorney from Norfolk County, urged the court to allow the cases to work their way through the system rather than dismiss them.

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“Do we just dismiss cases because it is hard?” she asked, arguing that each case should be reviewed on its individual merits. “We’re prepared to roll up our sleeves and do the work for each case.”

The justices peppered lawyers from both sides with questions and struggled with the issue for more than 90 minutes, an extraordinary amount of time for an appeals court hearing, which usually adheres to a time limit for arguments. It is not clear when the court will render a decision.

The decision should settle the legal arguments related to the Dookhan scandal, uncovered in 2012. Dookhan, a chemist with the state-run drug lab in Jamaica Plain, admitted that she tampered with drug evidence and served more than three years in prison.

The scandal sent the state’s criminal justice system scrambling, as defense lawyers argued that cases she was involved in were tainted and should be dismissed. Prosecutors argued that judges should look at each case individually, because in some cases a defendant could still be convicted based on other evidence.

In earlier rulings, the Supreme Judicial Court set guidelines on how the courts should handle the scandal and hear appeals in cases related to Dookhan. In one case the court found that judges should presume misconduct in any of the cases in which Dookhan was involved. The court asked prosecutors and defense lawyers to set up a system for all affected defendants to appeal.

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But the ACLU, working with the state’s public defender agency, called on the court Wednesday to dismiss all of the cases as a global remedy, saying the state has still failed to address more than 24,000 convictions that still hang over defendants in deportation proceedings, and in job and housing applications. Under their proposed resolution, all cases would be dismissed and prosecutors would face a deadline to decide which cases they want to retry.

Prosecutors have proposed notifying each defendant and alerting them to their right to appeal as a sufficient remedy. Letters were sent out to defendants in September, advising them of the process. But defense lawyers argued that the process has already gone on too long.

Justice Geraldine Hines asked Segal to define when it became “too late” to notify defendants of their rights. That happened last year, he said, when the state learned the number of cases that have still not been addressed.

Benjamin H. Keehn of the Committee for Public Counsel Services, the state’s public defender agency, added that it will be impossible to provide legal representation for all those affected, another reason for the court to use its authority to dismiss the cases.

O’Neil, the prosecutor, argued that the court should wait to see how many defendants want to appeal their cases and whether they will need lawyers, saying some defendants have chosen to move on with their lives and not appeal.

Hines took issue with that view, saying, “That makes it sound like a class of people just don’t care, and I can’t imagine that’s true.”

Justices David Lowy and Frank Gaziano, both recent appointments to the court with backgrounds as prosecutors, questioned whether the court needed to approve the global remedy and dismiss all the cases at once. Lowy questioned whether the state’s private defense lawyers would be willing to represent criminal defendants in their appeals, which would alleviate Keehn’s concerns that the defendants would not get adequate legal representation.And Gaziano asked whether a defendant should bear the burden of appealing a case if they feel an error was made.

Keehn argued to Lowy that defense lawyers have already stepped up to help defendants, but that it has not been enough. And he told Gaziano that the court should not compare a legal question of trial error to the severity of Dookhan’s “fraudulently induced criminal convictions.”

“It’s hard to put it in the same category of what we’re dealing with here,” Keehn said. “We’re talking about convicting people with fraudulent evidence. . . . It is hard to imagine a more damaging blow to the criminal justice system.”